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Crystal structure of the mouse CD1d in complex with the p99 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G08 PDB ENTRY 3G08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2M AMMONIUM TARTRATE AND 20% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.17 α = 90 b = 107.57 β = 90 c = 110.61 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 55 99.5 0.09 11.1 6.1 47272 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.6 0.83 2.4 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3G08 1.8 49.19 44833 2374 99.24 0.20681 0.20538 0.23361 0.2509 RANDOM
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.408 r_dihedral_angle_4_deg 16.478 r_dihedral_angle_3_deg 11.77 r_long_range_B_other 6.044 r_long_range_B_refined 6.042 r_dihedral_angle_1_deg 5.871 r_angle_refined_deg 1.267 r_mcangle_it 0.928 r_mcangle_other 0.927 r_scangle_other 0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.408 r_dihedral_angle_4_deg 16.478 r_dihedral_angle_3_deg 11.77 r_long_range_B_other 6.044 r_long_range_B_refined 6.042 r_dihedral_angle_1_deg 5.871 r_angle_refined_deg 1.267 r_mcangle_it 0.928 r_mcangle_other 0.927 r_scangle_other 0.905 r_angle_other_deg 0.899 r_scbond_it 0.566 r_scbond_other 0.553 r_mcbond_it 0.528 r_mcbond_other 0.528 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3007 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing